Variant report

Variant	rs17054295
Chromosome Location	chr3:54725202-54725203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10510771	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914973	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920788	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925949	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054291	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054293	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34590038	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55962540	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56063440	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59796966	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60303224	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61267487	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66795104	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67730102	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784130	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870690	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737517	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641640	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54713600-54743400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:54719000-54725400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:54724600-54726000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:54724800-54725800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:54724800-54726000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:54724800-54726400	Enhancers	Fetal Muscle Leg	muscle
7	chr3:54724800-54726600	Enhancers	Fetal Lung	lung
8	chr3:54725000-54725600	Enhancers	H9 Cell Line	embryonic stem cell
9	chr3:54725000-54725600	Enhancers	Fetal Stomach	stomach
10	chr3:54725000-54725600	Enhancers	Rectal Smooth Muscle	rectum
11	chr3:54725000-54725800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:54725000-54725800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:54725000-54726000	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:54725000-54726000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:54725000-54726600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:54725000-54726800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:54725200-54725600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:54725200-54725600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:54725200-54725600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:54725200-54725600	Enhancers	Brain Angular Gyrus	brain
21	chr3:54725200-54725600	Enhancers	Brain Hippocampus Middle	brain
22	chr3:54725200-54725800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:54725200-54725800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:54725200-54725800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr3:54725200-54725800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:54725200-54725800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:54725200-54725800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:54725200-54725800	Enhancers	HMEC	breast
29	chr3:54725200-54726800	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links